fixC:Gene Product(s): Difference between revisions

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Adding "length" to the physical properties table.
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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
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predicted oxidoreductase with FAD/NAD(P)-binding domain<ref name='LIB:Riley_2006'/>, B0043<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YaaS<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, FixC<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''predicted oxidoreductase with FAD/NAD(P)-binding domain<ref name='LIB:Riley_2006'/>, B0043<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YaaS<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, FixC<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK0044, JW0042, yaaS, b0043''
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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!|Qualifier!!GO ID!!GO term name!!Reference(s)!!Evidence Code!!with/from!!Aspect!!Notes!!Status
!|Qualifier!!GO ID!!GO term name!!Reference!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-  
|-  
|
|


|
|
GO:0016491
GO:0006810
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|
oxidoreductase activity
transport
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|
GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
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|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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|
InterPro:IPR001100<br />InterPro:IPR003042<br />InterPro:IPR006076<br />SP_KW:KW-0560
SP_KW:KW-0813
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|
F
P
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
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|
complete  
complete  
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|
|
GO:0006810
GO:0008152
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|
transport
metabolic process
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|
GO_REF:0000004
GOA:interpro<br />GO_REF:0000002
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|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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|
SP_KW:KW-0813
InterPro:IPR003042
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|
P
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
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|
complete  
complete  
|-  
|-  
|
|
 
|
|
GO:0042413
GO:0009437
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carnitine catabolic process  
carnitine metabolic process
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PMID:7473063
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|
IEP: Inferred from Expression Pattern
|
|
 
|
|
P  
P
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
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|
required fields missing 
complete
|-  
|-  
|
|


|
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GO:0008152
GO:0016491
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metabolic process
oxidoreductase activity
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GO_REF:0000002
GOA:interpro<br />GO_REF:0000002
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IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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InterPro:IPR003042
InterPro:IPR003042
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P
F
|
Seeded from [[EcoCyc]] (v14.0)
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complete
|-
|
 
|
GO:0016491
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oxidoreductase activity
|
GOA:interpro<br />GO_REF:0000002
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IEA: Inferred from Electronic Annotation
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InterPro:IPR006076
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F
|
Seeded from [[EcoCyc]] (v14.0)
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complete
|-
|
 
|
GO:0016491
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oxidoreductase activity
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GOA:spkw<br />SP_KW:GO_REF:0000004
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IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0560
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F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
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|
complete  
complete  
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electron transport chain
electron transport chain
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|
GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
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|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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P
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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oxidation reduction
oxidation reduction
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|
GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
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IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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P
P
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|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
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complete
|-
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GO:0050660
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FAD binding
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GO_REF:0000024
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ISA: Inferred from Sequence Alignment
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UniProtKB:P55931
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F
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PMID:4052375
PMID:17050691
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complete
|-
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GO:0051536
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iron-sulfur cluster binding
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GO_REF:0000024
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ISA: Inferred from Sequence Alignment
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UniProtKB:P55931
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F
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PMID:4052375
PMID:17050691
 
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complete
|-
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|
GO:0004174
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electron-transferring-flavoprotein dehydrogenase activity
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GO_REF:0000024
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ISA: Inferred from Sequence Alignment
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UniProtKB:P55931
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F
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PMID:4052375
PMID:17050691
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complete
|-
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GO:0009437
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carnitine metabolic process
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PMID:7473063
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IEP: Inferred from Expression Pattern
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|
P
|
The ''fixABCX'' operon is adjacent to and regulated similarity to the ''cai'' operon, which is necessary for carnitine metabolism <ref name='PMID:7815937'/>.
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complete  
complete  


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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
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Experiment(s):EBI-1135423<br />  
Experiment(s):EBI-1135423<br />  


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!|Compartment!!Description!!Evidence!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes


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!align=left {{table heading style}} |Name
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!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
45.7 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
45.703 kDa
|-
|-
!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
5.9 (calculated)
|-
|-
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
17420 - 17920 (calc based on 8 Y, 1 W, and 4 C residues)  
17,420 - 17,920 (calc based on 8 Y, 1 W, and 4 C residues)


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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span>
<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span><table>
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|- {{table heading style}}
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-
|
Domain
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7..87
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[http://pfam.janelia.org/family/PF01266 PF01266  FAD dependent oxidoreductase]
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PMID:19920124
|-
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Domain
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99..330
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[http://pfam.janelia.org/family/PF01266 PF01266  FAD dependent oxidoreductase]
|
 
|
PMID:19920124


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<td>
<!-- motifs column 2-->
<motif_map/>
</td>
</tr>
</table>


 
<table><tr valign='top'><td>
<span id="Structure"></span><big>'''Structure'''</big>
<span id='Structure'></span><big>'''Structure'''</big><br />
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|-
!align=left {{table heading style}} |Structures
!align=left {{table heading style}} |Structures
||
||
<beststructure>fixC
<beststructure>
562</beststructure>
gene=fixC
 
taxon=562,83333
</beststructure>
|-
|-
!align=left {{table heading style}} |Models
!align=left {{table heading style}} |Models
||
||
View models at:
View models at:
* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=fixC&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P68644 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=fixC&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P68644 PSI-PRED (P68644)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P68644 Genomes TO Protein (P68644)] (GTOP)
* [http://www.ebi.ac.uk/msd-srv/pqs/ Protein Quaternary Structure] (PQS)
* [http://spock.genes.nig.ac.jp/~genome/search.html Genomes TO Protein] (GTOP)


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<!--Structure_notes--></protect>
</td><td></protect>
==== Structure figures ====
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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===Notes===
===Notes===


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!|Resource type!!Source!!Notes/Reference
!|Resource type!!Source!!Notes/Reference


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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/16128037 GI:16128037]
|
Escherichia coli str. K-12 substr. MG1655
|-
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[[ASAP]]
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ASAP:ABE-0000149
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P68644 UniProtKB/Swiss-Prot:P68644]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:EG11564
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
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|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11564-MONOMER EcoCyc:EG11564-MONOMER]
EcoGene:EG11564
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
|
[[uniprot:P68644|UniProt:P68644]]
[http://www.ncbi.nlm.nih.gov/gene?term=948958 GeneID:948958]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://pfam.sanger.ac.uk/family?acc=PF01266 PFAM:PF01266]
RegulonDB:ECK120001517
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
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[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
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[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_414585 RefSeq:NP_414585]
[http://www.ncbi.nlm.nig.gov/protein/Array GeneID:948958]
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Escherichia coli str. K-12 substr. MG1655
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[http://modbase.compbio.ucsf.edu ModBase] ([[ModBase|EcoliWiki Page]])
[[EchoBASE]]
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[http://salilab.org/modbase/searchbyid?databaseID=P68644 ModBase:P68644]
EchoBASE:EB1525
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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==References==
==References==
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<references/>
<references />
__NOTOC__
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===Categories===
===Categories===
{{BacktoTop}}
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[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0042413_!_carnitine catabolic process]]

Latest revision as of 20:20, 17 February 2015

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

FixC

Synonyms

predicted oxidoreductase with FAD/NAD(P)-binding domain[1], B0043[2][1], YaaS[2][1], FixC[2][1] , ECK0044, JW0042, yaaS, b0043

Product description

flavoprotein (electron transport), possibly involved in anaerobic carnitine metabolism[2][3]

Related to carnitine metabolism; similarity to Rhizobium fix gene[4]

EC number (for enzymes)


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Notes

Function

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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0006810

transport

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0813

P

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003042

P

Seeded from EcoCyc (v14.0)

complete

GO:0009437

carnitine metabolic process

PMID:7473063[5]

IEP: Inferred from Expression Pattern

P

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003042

F

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006076

F

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

F

Seeded from EcoCyc (v14.0)

complete

GO:0022900

electron transport chain

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0249

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

P

Seeded from EcoCyc (v14.0)

complete

GO:0050660

FAD binding

GO_REF:0000024

ISA: Inferred from Sequence Alignment

UniProtKB:P55931

F

PMID:4052375[6] PMID:17050691[7]

complete

GO:0051536

iron-sulfur cluster binding

GO_REF:0000024

ISA: Inferred from Sequence Alignment

UniProtKB:P55931

F

PMID:4052375[6] PMID:17050691[7]

complete

GO:0004174

electron-transferring-flavoprotein dehydrogenase activity

GO_REF:0000024

ISA: Inferred from Sequence Alignment

UniProtKB:P55931

F

PMID:4052375[6] PMID:17050691[7]

complete

GO:0009437

carnitine metabolic process

PMID:7473063[5]

IEP: Inferred from Expression Pattern

P

The fixABCX operon is adjacent to and regulated similarity to the cai operon, which is necessary for carnitine metabolism [8].

complete

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

narH

PMID:16606699[9]

Experiment(s):EBI-1135423

Protein

dsbC

PMID:16606699[9]

Experiment(s):EBI-1135423

Protein

sdhA

PMID:16606699[9]

Experiment(s):EBI-1135423

Protein

ydjF

PMID:16606699[9]

Experiment(s):EBI-1135423

Protein

caiB

PMID:16606699[9]

Experiment(s):EBI-1135423

Protein

glnG

PMID:16606699[9]

Experiment(s):EBI-1135423

Protein

groL

PMID:16606699[9]

Experiment(s):EBI-1135423
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
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Notes

Structure and Physical Properties

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Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MSEDIFDAII VGAGLAGSVA ALVLAREGAQ VLVIERGNSA GAKNVTGGRL YAHSLEHIIP
GFADSAPVER LITHEKLAFM TEKSAMTMDY CNGDETSPSQ RSYSVLRSKF DAWLMEQAEE
AGAQLITGIR VDNLVQRDGK VVGVEADGDV IEAKTVILAD GVNSILAEKL GMAKRVKPTD
VAVGVKELIE LPKSVIEDRF QLQGNQGAAC LFAGSPTDGL MGGGFLYTNE NTLSLGLVCG
LHHLHDAKKS VPQMLEDFKQ HPAVAPLIAG GKLVEYSAHV VPEAGINMLP ELVGDGVLIA
GDAAGMCMNL GFTIRGMDLA IAAGEAAAKT VLSAMKSDDF SKQKLAEYRQ HLESGPLRDM
RMYQKLPAFL DNPRMFSGYP ELAVGVARDL FTIDGSAPEL MRKKILRHGK KVGFINLIKD
GMKGVTVL
Length

428

Mol. Wt

45.703 kDa

pI

5.9 (calculated)

Extinction coefficient

17,420 - 17,920 (calc based on 8 Y, 1 W, and 4 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Domain

7..87

PF01266 FAD dependent oxidoreductase

PMID:19920124[10]

Domain

99..330

PF01266 FAD dependent oxidoreductase

PMID:19920124[10]

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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=fixC taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16128037

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000149

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P68644

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11564

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11564

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948958

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001517

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948958

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1525

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 1.3 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 Eichler, K et al. (1995) The fix Escherichia coli region contains four genes related to carnitine metabolism. J. Basic Microbiol. 35 217-27 PubMed
  6. ↑ 6.0 6.1 6.2 Beckmann, JD & Frerman, FE (1985) Electron-transfer flavoprotein-ubiquinone oxidoreductase from pig liver: purification and molecular, redox, and catalytic properties. Biochemistry 24 3913-21 PubMed
  7. ↑ 7.0 7.1 7.2 Zhang, J et al. (2006) Structure of electron transfer flavoprotein-ubiquinone oxidoreductase and electron transfer to the mitochondrial ubiquinone pool. Proc. Natl. Acad. Sci. U.S.A. 103 16212-7 PubMed
  8. ↑ Eichler, K et al. (1994) Molecular characterization of the cai operon necessary for carnitine metabolism in Escherichia coli. Mol. Microbiol. 13 775-86 PubMed
  9. ↑ 9.0 9.1 9.2 9.3 9.4 9.5 9.6 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  10. ↑ 10.0 10.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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